Assembly of reads from metagenomic samples is a hard problem, often resulting in highly fragmented genome assemblies. Metagenomic binning allows us to reconstruct genomes by re-grouping the sequences by their organism of origin, thus representing a crucial processing step when exploring the biological diversity of metagenomic samples. Here we present Adversarial Autoencoders for Metagenomics Binning (AAMB), an ensemble deep learning approach that integrates sequence co-abundances and tetranucleotide frequencies into a common denoised space that enables precise clustering of sequences into microbial genomes. When benchmarked, AAMB presented similar or better results compared with the state-of-the-art reference-free binner VAMB, reconstructing ~7% more near-complete (NC) genomes across simulated and real data. In addition, genomes reconstructed using AAMB had higher completeness and greater taxonomic diversity compared with VAMB. Finally, we implemented a pipeline integrating VAMB and AAMB that enabled improved binning, recovering 20% and 29% more simulated and real NC genomes, respectively, compared to VAMB with moderate additional runtime. AAMB is freely available at https://github.com/RasmussenLab/VAMB.

Adversarial and variational autoencoders improve metagenomic binning